Hi Angela,I'm no expert but this question was answered some time ago by others. Look up the use of -rseed option for probtrackx2 through the forum archive. If you use multiple computers or parallel computing (cluster) you can have a smaller number of P which would reduce your calculation time. Taking 3 days to run with P = 5000 is normal on an average computer. The rseed value allows you to change the random number generator output allowing you to correctly add up all the different outputs with a smaller P (e.g running 10 Probtrackx2 runs at the same time using the cluster computers with only a P value of 500). If you just lower the P value without changing the rseed value you're not actually benefiting from adding the results of multiple simultaneous runs.
Others with more experience can correct or supplement this answer if necessary.
Hope this helps.
Jon
-------- Original message --------
From: Angela Favaro <[log in to unmask]>
Date: 05-23-2016 3:52 AM (GMT-05:00)
To: [log in to unmask]
Subject: [FSL] probtrackX2
Dear all,
Sorry to repeat my question, but I received no message in reply to my previous mail (is it not appropriate in some way?)
I am testing the command line below and the first matrix needed more than 3 days for output.
I would like to have some suggestion on how to speed out the process (if at all possible) or to know if this is due to something wrong in my command line
probtrackx2 --network -x ${subject}/masks_surface.txt -V 1 --omatrix1 -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -s ${subject}/dti.bedpostX/merged -m ${subject}/dti.bedpostX/nodif_brain_mask --dir=${subject}/track_graph --avoid=${subject}/dti/anat/ventricles.nii.gz --xfm=${subject}/dti.bedpostX/xfms/fs2fa.mat --seedref=${subject}/dti/anat/fs.nii.gz --waypoints=${subject}/dti/waypoints.txt --waycond='OR' --meshspace=freesurfer
masks.txt, ventricles and wm.lh wm.rh (waypoints) are all in Freesurfer's space (fs)
fs2fa.mat was created as suggested in the fsl site
the aim is to create a matrix to be used for graph analysis. Do I have to use the option --onewaycondition? this point is not clear to me
Thank you again for any help!
Angela
Dear FSL experts,
I need some help in using probtrackx2.
I want to use Destrieux parcellation surfaces obtained by using Freesurfer (and some subcortical areas) to perform probabilistic tracking in order to create a matrix to perform graph analyses.
I looked at the instructions and previous posting and I am trying with this command line (in a script):
probtrackx2 --network -x ${dir}/${subject}/dti/masks.txt -V 1 --omatrix1 -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -s ${dir}/${subject}/dti.bedpostX/merged -m ${dir}/${subject}/dti.bedpostX/nodif_brain_mask --dir=${dir}/${subject}/track_graph --avoid=${dir}/${subject}/dti/anat/ventricles.nii.gz --xfm=${dir}/${subject}/dti.bedpostX/xfms/fs2fa.mat --seedref=${dir}/${subject}/dti/anat/fs.nii.gz --waypoints=${dir}/${subject}/dti/waypoints.txt --waycond='OR' --meshspace=freesurfer
masks.txt is a list of all masks created by Freesurfer (with the commands mri_annotation2label and mri_label2vol) and so they are in Freesurfer's space (fs)
ventricles and wm.lh wm.rh (as well as subcortical nuclei) were obtained with the command mri_binarize (wm.lh are wm.rh are waypoints.txt) and are in Freesurfer's space
is this command correct? do I have to also include the inverse matrix? ----invxfm=xfms/fa2fs ?
is it correct the option --waycond='OR'
do I have to use the option --onewaycondition ?
please give some help! this is a very complex issue and I do not want to make mistakes (and loose hours of computation....)
Thank you!
Angela
